SeqNjoy: Complete RNA-Seq workflows in your Desktop

The RNA-Seq GUI

SeqNjoy is a stand-alone application for generating and analyzing differential gene expression results from RNA-Seq experiments. Analyses can be performed from the very initial step, using the files containing short reads (FASTQ files), or from an intermediate stage, using already aligned reads in BAM/SAM files.

The main results of SeqNjoy are annotated list of genes differentially expressed (or not) between groups of samples. These results are presented both as standard tables and as interactive pages that allow the user to apply custom filters and to download ready-to-publish figures (scatter-plots).

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Computer Requirements

	Minimum	Recommended
Architecture	64-bit
Operative System	Windows, macOS, Linux (Debian or Fedora-based)
Web Browser	Chrome, Firefox, Safari, Edge
RAM Memory	8 GB	16 GB
Hard Disk	500 GB	1 TB

• Minimum requirements are adequate for bacterial genomes. Recommended requirements are adequate also for eukaryotic genomes.
• Some of the steps performed by SeqNjoy may take many hours to complete. It is recommended to run the application with no other intensive processes consumming CPU or RAM memory.
  Please disable Sleep Mode or Hibernation in your computer to avoid interruptions of long lasting processes
• Hard drive requirements specify the necessary storage space for project files in typical RNA-Seq analysis. SeqNjoy is installed as a standard R package, and users can store project folders on local or USB-connected hard drives of their choice.

Installation

In addition to installing R, SeqNjoy has specific software requirements that vary by operating system. Please refer to the help section to ensure you meet all necessary requirements.

Then, open R and follow the detailed installation instructions:

• From GitHub
• From Source

Resources

• Help Pages
• Quick Guide and RNA-Seq Sample Files to start using SeqNjoy
• Source code: GitHub

License

Copyright 2022 BioinfoGP (CNB-CSIC). All rights reserved.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License 3 as published by the Free Software Foundation, either version 3 of the License, or any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You can read the full GNU General Public License here.

Credits

• Authors: Juan Antonio García-Martín, Rafael Torres-Pérez and Juan Carlos Oliveros
• Please cite: Juan A Garcia-Martin, Rafael Torres-Perez and Juan C Oliveros (2022) SeqNjoy: Complete RNA-Seq workflows in your Desktop. (Manuscript in preparation)
• Contact: bioinfogp@cnb.csic.es